Essential fatty acid research has shown that omega-3 fatty acids such as eicosahexaenoic acid (EPA) and docoshexaenoic acid (DHA; 22:6n3) may help maintain normal body structure, function and aid in long-term health and wellbeing. Common sources of omega 3 fatty acids include flax seed, fish oil, fishmeal, and more recently, purpose grown algae. This commercially produced source of omega 3 fatty acids has been evaluated as a supplement to animal diets and for its impact on metabolism; however, questions regarding the effect of processing and storage in pet foods are unanswered. The objective was to determine the effect of processing on stability of an algal source of DHA, (DHAgold S17-B; DSM Nutritional Products) added to the diet by premix, extrusion-drying processing, and extended storage. Three nutritionally complete pet diets at protein levels 21.7, 25, and 30% CP (Low, Medium and High, respectively) were produced with equal levels of DHA supplied by DHAgold S17-B, fishmeal and fish oil. Diets were produced on a Wenger X-20 single screw extruder (Wenger Mfg, Sabetha, KS) and dried at 104°C for 10 min at each pass in a triple pass dryer (Wenger Mfg, Sabetha, KS). Samples from each treatment were analyzed immediately following production for moisture and fatty acids. Shelf-life samples were collected in whirlpaks with a pin-hole and stored at 40°C and 75% relative humidity for analysis at 3, 6, 12, 18 and 24 weeks following production. Retention of EPA and DHA at production time was not affected by CP level (P > 0.05), but was impacted by DHA source (P < 0.05). The total omega 3 fatty acids were affected by DHA source and CP level (P < 0.05). As time in storage progressed through 0, 3, 6, 12, 18 and 24 weeks EPA (P < 0.05; 12.53, 10.45, 10.19, 8.9, 8.4, and 8.2 mg/kg, respectively) and DHA (P < 0.05; 7.7, 7.2, 6.9, 6.1, 6.4, and 6.0 mg/kg, respectively) declined slightly; but, total omega 3 fatty acids (P < 0.05; 35.6, 47.7, 47.9, 44.4, 43.3, and 41.8 mg/kg, respectively) were greater at all times than the start. These results suggest that elevated temperatures during storage for 24 weeks could result in slight EPA and DHA sacrifice. DHAgold S17-B appears to be a stable source of DHA when compared with fish oil and fishmeal.